NPASS Compound

Structure

NPC3621 OpenBabel06302216182D 27 29 0 0 1 0 0 0 0 0999 V2000 0.8660 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 27 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 21 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 26 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 24 1 0 0 0 0 9 21 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 23 1 6 0 0 0 11 12 1 0 0 0 0 11 22 1 6 0 0 0 12 13 1 1 0 0 0 12 20 1 0 0 0 0 13 18 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 19 1 0 0 0 0 17 18 1 0 0 0 0 20 21 1 0 0 0 0 24 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	372.16
Volume:	380.389
LogP:	3.53
LogD:	3.009
LogS:	-3.035
# Rotatable Bonds:	4
TPSA:	99.38
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.616
Synthetic Accessibility Score:	3.807
Fsp3:	0.333
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.946
MDCK Permeability:	9.807462447497528e-06
Pgp-inhibitor:	0.003
Pgp-substrate:	0.23
Human Intestinal Absorption (HIA):	0.012
20% Bioavailability (F20%):	0.669
30% Bioavailability (F30%):	0.025

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.073
Plasma Protein Binding (PPB):	95.40896606445312%
Volume Distribution (VD):	0.828
Pgp-substrate:	8.38915729522705%

ADMET: Metabolism

CYP1A2-inhibitor:	0.076
CYP1A2-substrate:	0.392
CYP2C19-inhibitor:	0.276
CYP2C19-substrate:	0.48
CYP2C9-inhibitor:	0.475
CYP2C9-substrate:	0.961
CYP2D6-inhibitor:	0.749
CYP2D6-substrate:	0.434
CYP3A4-inhibitor:	0.142
CYP3A4-substrate:	0.236

ADMET: Excretion

Clearance (CL):	13.184
Half-life (T1/2):	0.67

ADMET: Toxicity

hERG Blockers:	0.066
Human Hepatotoxicity (H-HT):	0.18
Drug-inuced Liver Injury (DILI):	0.049
AMES Toxicity:	0.037
Rat Oral Acute Toxicity:	0.222
Maximum Recommended Daily Dose:	0.065
Skin Sensitization:	0.569
Carcinogencity:	0.053
Eye Corrosion:	0.003
Eye Irritation:	0.037
Respiratory Toxicity:	0.063

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC3621

Natural Product ID:	NPC3621
*Common Name:**	UZKPAEYMUOTYEF-SLFFLAALSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UZKPAEYMUOTYEF-SLFFLAALSA-N
Standard InCHI:	InChI=1S/C21H24O6/c1-11(2)4-9-14-15(23)10-16(26-3)17-18(24)19(25)20(27-21(14)17)12-5-7-13(22)8-6-12/h4-8,10,18-20,22-25H,9H2,1-3H3/t18-,19-,20+/m0/s1
SMILES:	CC(=CCc1c(cc(c2[C@@H]([C@@H]([C@@H](c3ccc(cc3)O)Oc12)O)O)OC)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44257163
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0003642] 8-prenylated flavans

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO19141	Aframomum melegueta	Species	Zingiberaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[22789014]
NPO7385	Schisandra sphenanthera	Species	Schisandraceae	Eukaryota	fruits	n.a.	n.a.	PMID[23265871]
NPO8415	Tetragonotheca ludoviciana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23501116]
NPO7385	Schisandra sphenanthera	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7385	Schisandra sphenanthera	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7385	Schisandra sphenanthera	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7385	Schisandra sphenanthera	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO470	Prismatomeris connata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19141	Aframomum melegueta	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3435	Saussurea katochaete	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6728	Rubus niveus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3268	Callyspongia flammea	Species	Callyspongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7941	Marshallia obovata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1953	Miltochrista calamina	Species	Erebidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3848	Myrtopsis macrocarpa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1513	Penicillium nalgiovense	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4821	Hypselodoris infucata	Species	Chromodorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4194	Teucrium buxifolium	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7385	Schisandra sphenanthera	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8415	Tetragonotheca ludoviciana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3089	Cistus villosus	Species	Cistaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC3621 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	380
0.1-0.2	1413
0.2-0.3	4014
0.3-0.4	10991
0.4-0.5	7603
0.5-0.6	3882
0.6-0.7	6670
0.7-0.8	5885
0.8-0.85	1278
0.85-0.9	409
0.9-0.95	155
0.95-1	17

Similarity Score	Similarity Level	Natural Product ID

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC3621 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	326
0.1-0.2	848
0.2-0.3	1754
0.3-0.4	2642
0.4-0.5	1728
0.5-0.6	961
0.6-0.7	696
0.7-0.8	171
0.8-0.85	15
0.85-0.9	6
0.9-0.95	3
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data